Crystal structure of Phm7 in complex with inhibitor

Experimental Data Snapshot

  • Resolution: 1.61 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.183 

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This is version 1.2 of the entry. See complete history


Molecular Basis for Two Stereoselective Diels-Alderases that Produce Decalin Skeletons*.

Fujiyama, K.Kato, N.Re, S.Kinugasa, K.Watanabe, K.Takita, R.Nogawa, T.Hino, T.Osada, H.Sugita, Y.Takahashi, S.Nagano, S.

(2021) Angew Chem Int Ed Engl 60: 22401-22410

  • DOI: https://doi.org/10.1002/anie.202106186
  • Primary Citation of Related Structures:  
    7E5T, 7E5U, 7E5V

  • PubMed Abstract: 

    Enzymes catalyzing [4+2] cycloaddition have attracted increasing attention because of their key roles in natural product biosynthesis. Here, we solved the X-ray crystal structures of a pair of decalin synthases, Fsa2 and Phm7, that catalyze intramolecular [4+2] cycloadditions to form enantiomeric decalin scaffolds during biosynthesis of the HIV-1 integrase inhibitor equisetin and its stereochemical opposite, phomasetin. Computational modeling, using molecular dynamics simulations as well as quantum chemical calculations, demonstrates that the reactions proceed through synergetic conformational constraints assuring transition state-like substrates folds and their stabilization by specific protein-substrate interactions. Site-directed mutagenesis experiments verified the binding models. Intriguingly, the flexibility of bound substrates is largely different in two enzymes, suggesting the distinctive mechanism of dynamics regulation behind these stereoselective reactions. The proposed reaction mechanism herein deepens the basic understanding how these enzymes work but also provides a guiding principle to create artificial enzymes.

  • Organizational Affiliation

    Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyama-cho, Minami, Tottori, 680-8552, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C
389Pyrenochaetopsis sp.Mutation(s): 0 
Gene Names: phm7
Find proteins for A0A2Z5XAU0 (Pyrenochaetopsis sp)
Explore A0A2Z5XAU0 
Go to UniProtKB:  A0A2Z5XAU0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2Z5XAU0
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HZC (Subject of Investigation/LOI)
Query on HZC

Download Ideal Coordinates CCD File 
D [auth A]
I [auth B]
J [auth B]
K [auth B]
S [auth C]
D [auth A],
I [auth B],
J [auth B],
K [auth B],
S [auth C],
T [auth C],
U [auth C]
C11 H23 N
Query on SO4

Download Ideal Coordinates CCD File 
BA [auth C]
CA [auth C]
H [auth A]
O [auth B]
P [auth B]
BA [auth C],
CA [auth C],
H [auth A],
O [auth B],
P [auth B],
Q [auth B]
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth C]
E [auth A]
F [auth A]
G [auth A]
L [auth B]
AA [auth C],
E [auth A],
F [auth A],
G [auth A],
L [auth B],
M [auth B],
N [auth B],
R [auth B],
V [auth C],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.61 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.183 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.052α = 90
b = 149.881β = 97.119
c = 99.27γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
pointlessdata scaling
Aimlessdata scaling
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan19H04665
Japan Society for the Promotion of Science (JSPS)Japan19H05780
Japan Society for the Promotion of Science (JSPS)Japan19H04658

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-30
    Type: Initial release
  • Version 1.1: 2021-10-13
    Changes: Database references
  • Version 1.2: 2024-04-03
    Changes: Data collection, Derived calculations, Refinement description